Using Bioconda with Mac M1 Processor?

Question

[williamdurstock]

Hello Everyone!

I'm extremely new to bioinformatics, so please understand my complete ignorance to this process.

My lab use to utilize Michigan States Ribosomal Database Project (RDP), but it recently stopped being supported and is no longer available.

We are attempting to pivot to QIIME 2 to clean up and process illumina base-paired sequences.

I'll get straight to the problem.

So far i downloaded the latest version of Anaconda 3.

From what i have researched, i should be able to use commands to download bioconda, QIIME2, and DADA2.

When i give commands, i get this error.

(base) William@Mirzas-iMac ~ % cd anaconda3
(base) William@Mirzas-iMac anaconda3 % conda activate myenv
(myenv) William@Mirzas-iMac anaconda3 % conda install -c bioconda bioconductor-dada2
Retrieving notices: ...working... done
Collecting package metadata (current_repodata.json): done
Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - bioconductor-dada2

Current channels:

  - https://conda.anaconda.org/bioconda/osx-arm64
  - https://conda.anaconda.org/bioconda/noarch
  - https://conda.anaconda.org/conda-forge/osx-arm64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/osx-arm64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-arm64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

No matter what I try to download, I get the same error. Has anyone any information on this in relation to the new Mac silicone processor?

Answer 1

[John Marshall]

Apple Silicon Macs have now been available for 2½ years. Perhaps Bioconda will share their plans to support osx-arm64 sometime…

In the meantime, if you have Rosetta 2 installed, with luck you can you can install and use x86-targetted tools via conda as follows:

CONDA_SUBDIR=osx-64 conda create -n myenv bioconductor-dada2

as described in slightly more detail in this comment.

[williamdurstock]

Thank you John! I'll try that and update later.